+++ /dev/null
---------------------------------------------------------------------------------
- FILE ASSIGNMENT
---------------------------------------------------------------------------------
- Input file : 1L2Y_MD.inp
- Output file : 1L2Y_MD.out_GB000
-
- Sidechain potential file :
- /users/pk376/unres-git/unres/PARAM/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_ga
- p8g-sc
- SCp potential file : /users/pk376/unres-git/unres/PARAM/scp.parm
- Electrostatic potential file :
- /users/pk376/unres-git/unres/PARAM/electr_631Gdp.parm
- Cumulant coefficient file :
- /users/pk376/unres-git/unres/PARAM/fourier_opt.parm.1igd_hc_iter3_3
- Torsional parameter file :
- /users/pk376/unres-git/unres/PARAM/torsion_631Gdp.parm
- Double torsional parameter file :
- /users/pk376/unres-git/unres/PARAM/torsion_double_631Gdp.parm
- SCCOR parameter file : /users/pk376/unres-git/unres/PARAM/sccor_pdb_shelly.dat
- Bond & inertia constant file : /users/pk376/unres-git/unres/PARAM/bond.parm
- Bending parameter file :
- /users/pk376/unres-git/unres/PARAM/thetaml.5parm
- Rotamer parameter file :
- /users/pk376/unres-git/unres/PARAM/scgauss.parm
- Threading database :
- /users/pk376/unres-git/unres/PARAM/patterns.cart
---------------------------------------------------------------------------------
-********************************************************************************
-United-residue force field calculation - parallel job.
-********************************************************************************
- ### LAST MODIFIED 03/28/12 23:29 by czarek
- ++++ Compile info ++++
- Version 2.5 build 302
- compiled Mon Jul 23 17:42:12 2012
- compiled by jal47@matrix.chem.cornell.edu
- OS name: Linux
- OS release: 2.6.34.9-69.fc13.x86_64
- OS version: #1 SMP Tue May 3 09:23:03 UTC 2011
- flags:
- INSTALL_DIR = /users/software/mpich-1.2.7p1_int...
- FC= ifort
- OPT = -g -ip -w -CB
- FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
- FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...
- FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
- FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report ...
- LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...
- ARCH = LINUX
- PP = /lib/cpp -P
- object = unres.o arcos.o cartprint.o chainbuild...
- GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES ...
- GAB: BIN = ../../../bin/unres/MD/unres_ifort_MP...
- E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNR...
- E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort...
- ++++ End of compile info ++++
-
-Potential is GB , exponents are 6 12
-
-Disulfide bridge parameters:
-S-S bridge energy: -5.50
-d0cm: 3.78 akcm: 15.10
-akth: 11.00 akct: 12.00
-v1ss: -1.08 v2ss: 7.61 v3ss: 13.70
- MPI: node= 0 iseed(4)= 0 0 -46
- -45086
- ran_num 6.422640197456531E-013
-RMSDBC = 3.0
-RMSDBC1 = 0.5
-RMSDBC1MAX = 1.5
-DRMS = 0.1
-RMSDBCM = 3.0
-Time limit (min): 960.0
- RESCALE_MODE 2
-Library routine used to diagonalize matrices.
-
-=========================== Parameters of the MD run ===========================
-
-The units are:
-positions: angstrom, time: 48.9 fs
-velocity: angstrom/(48.9 fs), acceleration: angstrom/(48.9 fs)**2
-energy: kcal/mol, temperature: K
-
- Number of time steps: 1000000
- Initial time step of numerical integration: 0.10000 natural units
- 4.89000 fs
-A-MTS algorithm used; initial time step for fast-varying short-range forces split into 1 steps.
-Short-range force cutoff 2.00 lambda 0.30
-Maximum acceleration threshold to reduce the time step/increase split number: 10.00000
-Maximum predicted energy drift to reduce the timestep/increase split number: 10.00000
- Maximum velocity threshold to reduce velocities: 20.00000
- Frequency of property output: 10000
- Frequency of coordinate output: 10000
-Nose-Hoover bath calculation
-Mol.Phys. 87 1117 (1996) Martyna et al.
-NVT-XI-RESPA algorithm
- Temperature: 300.00000
- Q = 1.00000
-
-============================== End of MD run setup =============================
-
-
-Energy-term weights (unscaled):
-
-WSCC= 1.352790 (SC-SC)
-WSCP= 1.593040 (SC-p)
-WELEC= 0.715340 (p-p electr)
-WVDWPP= 0.113710 (p-p VDW)
-WBOND= 1.000000 (stretching)
-WANG= 1.138730 (bending)
-WSCLOC= 0.162580 (SC local)
-WTOR= 1.985990 (torsional)
-WTORD= 1.570690 (double torsional)
-WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
-WEL_LOC= 0.160360 (multi-body 3-rd order)
-WCORR4= 0.428870 (multi-body 4th order)
-WCORR5= 0.000000 (multi-body 5th order)
-WCORR6= 0.000000 (multi-body 6th order)
-WSCCOR= 0.000000 (back-scloc correlation)
-WTURN3= 1.687220 (turns, 3rd order)
-WTURN4= 0.662300 (turns, 4th order)
-WTURN6= 0.000000 (turns, 6th order)
-
-Hydrogen-bonding correlation between contact pairs of peptide groups
-
-Scaling factor of 1,4 SC-p interactions: 0.400
-General scaling factor of SC-p interactions: 1.000
-
-Energy-term weights (scaled):
-
-WSCC= 1.352790 (SC-SC)
-WSCP= 1.593040 (SC-p)
-WELEC= 0.715340 (p-p electr)
-WVDWPP= 0.113710 (p-p VDW)
-WBOND= 1.000000 (stretching)
-WANG= 1.138730 (bending)
-WSCLOC= 0.162580 (SC local)
-WTOR= 1.985990 (torsional)
-WTORD= 1.570690 (double torsional)
-WSTRAIN= 1.000000 (SS bridges & dist. cnstr.)
-WEL_LOC= 0.160360 (multi-body 3-rd order)
-WCORR4= 0.428870 (multi-body 4th order)
-WCORR5= 0.000000 (multi-body 5th order)
-WCORR6= 0.000000 (multi-body 6th order)
-WSCCOR= 0.000000 (back-scloc correlatkion)
-WTURN3= 1.687220 (turns, 3rd order)
-WTURN4= 0.662300 (turns, 4th order)
-WTURN6= 0.000000 (turns, 6th order)
- Reference temperature for weights calculation: 300.000000000000
- Parameters of the SS-bond potential:
- D0CM 3.78000000000000 AKCM 15.1000000000000 AKTH
- 11.0000000000000 AKCT 12.0000000000000
- V1SS -1.08000000000000 V2SS 7.61000000000000 V3SS
- 13.7000000000000
- EBR -5.50000000000000
-PDB data will be read from file ../../../1L2Y.pdb
- Nres: 21
-Backbone and SC coordinates as read from the PDB
- 1 21 D -9.841 4.399 -5.051 -9.841 4.399 -5.051
- 2 14 ASN -8.608 3.135 -1.618 -10.407 3.153 -2.437
- 3 5 LEU -4.923 4.002 -2.452 -4.618 6.091 -1.850
- 4 8 TYR -3.690 2.738 0.981 -1.959 3.143 3.797
- 5 4 ILE -5.857 -0.449 0.613 -7.484 -0.369 1.074
- 6 13 GLN -4.122 -1.167 -2.743 -5.089 -1.450 -4.853
- 7 7 TRP -0.716 -0.631 -0.993 1.727 0.440 1.450
- 8 5 LEU -1.641 -2.932 1.963 -2.244 -2.097 3.799
- 9 19 LYS -3.024 -5.791 -0.269 -3.820 -5.527 -3.146
- 10 16 ASP 0.466 -6.016 -1.905 0.653 -5.125 -3.676
- 11 10 GLY 2.060 -6.618 1.593 2.060 -6.618 1.593
- 12 10 GLY 2.626 -2.967 2.723 2.626 -2.967 2.723
- 13 20 PRO 6.333 -2.533 3.806 5.724 -2.372 5.058
- 14 12 SER 7.049 -6.179 2.704 6.757 -6.938 3.675
- 15 12 SER 6.389 -5.315 -1.015 5.245 -5.350 -1.546
- 16 10 GLY 9.451 -3.116 -1.870 9.451 -3.116 -1.870
- 17 18 ARG 7.289 0.084 -2.054 5.225 -1.826 -3.986
- 18 20 PRO 6.782 3.088 0.345 7.458 3.741 -0.688
- 19 20 PRO 3.287 4.031 1.686 4.025 4.206 2.856
- 20 20 PRO 1.185 6.543 -0.353 0.358 5.421 -0.430
- 21 12 SER 0.852 10.027 1.285 1.151 10.636 1.488
- 22 21 D -1.250 12.539 -0.754 -1.250 12.539 -0.754
-nsup= 20 nstart_sup= 2
- ITEL
- 1 21 0
- 2 14 1
- 3 5 1
- 4 8 1
- 5 4 1
- 6 13 1
- 7 7 1
- 8 5 1
- 9 19 1
- 10 16 1
- 11 10 1
- 12 10 2
- 13 20 1
- 14 12 1
- 15 12 1
- 16 10 1
- 17 18 2
- 18 20 2
- 19 20 2
- 20 20 1
- 21 12 0
- ns= 0 iss:
-Boundaries in phi angle sampling:
-D 1 -180.0 180.0
-ASN 2 -180.0 180.0
-LEU 3 -180.0 180.0
-TYR 4 -180.0 180.0
-ILE 5 -180.0 180.0
-GLN 6 -180.0 180.0
-TRP 7 -180.0 180.0
-LEU 8 -180.0 180.0
-LYS 9 -180.0 180.0
-ASP 10 -180.0 180.0
-GLY 11 -180.0 180.0
-GLY 12 -180.0 180.0
-PRO 13 -180.0 180.0
-SER 14 -180.0 180.0
-SER 15 -180.0 180.0
-GLY 16 -180.0 180.0
-ARG 17 -180.0 180.0
-PRO 18 -180.0 180.0
-PRO 19 -180.0 180.0
-PRO 20 -180.0 180.0
-SER 21 -180.0 180.0
-D 22 -180.0 180.0
-nsup= 20
- nsup= 20 nstart_sup= 2 nstart_seq= 2
- NZ_START= 2 NZ_END= 21
- IZ_SC= 0
- Contact order: 0.308441558441558
- Shifting contacts: 2 2
- 1 ILE 5 ASN 2
- 2 TRP 7 TYR 4
- 3 LEU 8 TYR 4
- 4 LEU 8 ILE 5
- 5 LYS 9 GLN 6
- 6 GLY 12 TRP 7
- 7 GLY 12 LEU 8
- 8 SER 14 GLY 11
- 9 SER 15 ASP 10
- 10 SER 15 GLY 11
- 11 PRO 19 TRP 7
- 12 PRO 20 LEU 3
- 13 PRO 20 TYR 4
- 14 PRO 20 TRP 7
-Extended chain initial geometry.
-
-Geometry of the virtual chain.
- Res d Theta Gamma Dsc Alpha Beta
-D 1 0.000 0.000 0.000 0.000 0.000 0.000
-ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
-LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
-TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
-ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
-GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
-TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
-LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
-LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
-ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
-GLY 11 3.800 90.000 180.000 0.000 110.000 -120.000
-GLY 12 3.800 90.000 180.000 0.000 110.000 -120.000
-PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
-SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
-SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
-GLY 16 3.800 90.000 180.000 0.000 110.000 -120.000
-ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
-PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
-PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
-PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
-SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
-D 22 3.800 90.000 180.000 0.000 0.000 0.000
-
-
-********************************************************************************
- Processor 0: end reading molecular data.
-********************************************************************************
-
-
-Mesoscopic molecular dynamics (MD) calculation.
-
-********************************************************************************
-
- Calling chainbuild
-====================MD calculation start====================
- Initial velocities randomly generated
- Initial velocities
- 0 0.02267 0.06282 -0.18129 0.00000 0.00000 0.00000
- 1 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
- 2 -0.36014 -0.22705 -0.00171 -0.06904 -0.02446 0.24778
- 3 0.27655 0.20645 0.14150 0.26200 0.15105 0.09342
- 4 0.10834 -0.11941 0.14712 0.10330 -0.09595 0.03277
- 5 0.05798 -0.08974 0.08325 0.03879 0.02648 -0.14707
- 6 0.01211 0.16444 -0.14711 -0.01628 0.11599 -0.16511
- 7 -0.01010 -0.05513 0.03662 -0.18958 0.06429 0.04531
- 8 -0.01799 0.13439 -0.04510 0.02318 0.10657 0.03722
- 9 -0.26458 -0.01929 0.09531 -0.22533 -0.17075 -0.04594
- 10 0.14062 -0.06051 -0.18363 0.20415 -0.15549 -0.17329
- 11 -0.14145 0.13159 -0.00733 0.00000 0.00000 0.00000
- 12 0.19745 -0.24261 0.01759 0.00000 0.00000 0.00000
- 13 -0.15305 0.28008 0.07251 0.06558 0.14824 0.10057
- 14 0.11104 -0.31941 0.15684 -0.02949 -0.09688 0.05398
- 15 0.14534 0.10342 -0.23754 -0.13923 0.07952 0.07655
- 16 -0.11969 0.14757 0.15002 0.00000 0.00000 0.00000
- 17 -0.09007 -0.15856 -0.20234 -0.07955 -0.08516 -0.10245
- 18 0.24139 0.09063 0.14043 -0.02074 0.10220 0.04907
- 19 -0.14354 -0.07226 -0.29143 -0.12408 -0.06855 -0.02978
- 20 0.28536 0.09023 0.56577 0.02348 0.16297 0.19270
- 21 0.00000 0.00000 0.00000 -0.13725 -0.06434 -0.21957
- 22 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
- Calling the zero-angular momentum subroutine
- vcm right after adjustment:
- 1.837610523517500E-017 -2.960594732333751E-018 9.596410511702503E-018
-
-
- alpha-carbon coordinates centroid coordinates
- X Y Z X Y Z
-D ( 1) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
-ASN( 2) 3.80000 0.00000 0.00000 3.64779 0.96674 1.37044
-LEU( 3) 3.80000 -3.80000 0.00000 2.68687 -3.62474 -1.57795
-TYR( 4) 7.60000 -3.80000 0.00000 7.37548 -2.37399 2.02147
-ILE( 5) 7.60000 -7.60000 0.00000 6.58044 -7.43947 -1.44530
-GLN( 6) 11.40000 -7.60000 0.00000 11.19753 -6.31407 1.82291
-TRP( 7) 11.40000 -11.40000 0.00000 9.90453 -11.16454 -2.11994
-LEU( 8) 15.20000 -11.40000 0.00000 15.02474 -10.28687 1.57795
-LYS( 9) 15.20000 -15.20000 0.00000 13.74127 -14.97033 -2.06786
-ASP( 10) 19.00000 -15.20000 0.00000 18.84553 -14.21890 1.39078
-GLY( 11) 19.00000 -19.00000 0.00000 19.00000 -19.00000 0.00000
-GLY( 12) 22.80000 -19.00000 0.00000 22.80000 -19.00000 0.00000
-PRO( 13) 22.80000 -22.80000 0.00000 22.02787 -22.67843 -1.09456
-SER( 14) 26.60000 -22.80000 0.00000 26.49606 -22.13981 0.93587
-SER( 15) 26.60000 -26.60000 0.00000 25.93981 -26.49606 -0.93587
-GLY( 16) 30.40000 -26.60000 0.00000 30.40000 -26.60000 0.00000
-ARG( 17) 30.40000 -30.40000 0.00000 28.66629 -30.12703 -2.45767
-PRO( 18) 34.20000 -30.40000 0.00000 34.07843 -29.62787 1.09456
-PRO( 19) 34.20000 -34.20000 0.00000 33.42787 -34.07843 -1.09456
-PRO( 20) 38.00000 -34.20000 0.00000 37.87843 -33.42787 1.09456
-SER( 21) 38.00000 -38.00000 0.00000 37.33981 -37.89606 -0.93587
-D ( 22) 41.80000 -38.00000 0.00000 41.80000 -38.00000 0.00000
-
-Geometry of the virtual chain.
- Res d Theta Gamma Dsc Alpha Beta
-D 1 0.000 0.000 0.000 0.000 0.000 0.000
-ASN 2 3.800 0.000 0.000 1.684 110.000 -120.000
-LEU 3 3.800 90.000 0.000 1.939 110.000 -120.000
-TYR 4 3.800 90.000 180.000 2.484 110.000 -120.000
-ILE 5 3.800 90.000 180.000 1.776 110.000 -120.000
-GLN 6 3.800 90.000 180.000 2.240 110.000 -120.000
-TRP 7 3.800 90.000 180.000 2.605 110.000 -120.000
-LEU 8 3.800 90.000 180.000 1.939 110.000 -120.000
-LYS 9 3.800 90.000 180.000 2.541 110.000 -120.000
-ASP 10 3.800 90.000 180.000 1.709 110.000 -120.000
-GLY 11 3.800 90.000 180.000 0.000 180.000 180.000
-GLY 12 3.800 90.000 180.000 0.000 180.000 180.000
-PRO 13 3.800 90.000 180.000 1.345 110.000 -120.000
-SER 14 3.800 90.000 180.000 1.150 110.000 -120.000
-SER 15 3.800 90.000 180.000 1.150 110.000 -120.000
-GLY 16 3.800 90.000 180.000 0.000 180.000 180.000
-ARG 17 3.800 90.000 180.000 3.020 110.000 -120.000
-PRO 18 3.800 90.000 180.000 1.345 110.000 -120.000
-PRO 19 3.800 90.000 180.000 1.345 110.000 -120.000
-PRO 20 3.800 90.000 180.000 1.345 110.000 -120.000
-SER 21 3.800 90.000 180.000 1.150 110.000 -120.000
-D 22 3.800 90.000 180.000 0.000 180.000 180.000
- H0= 122.583635723249
- Potential energy and its components
-
-Virtual-chain energies:
-
-EVDW= -1.680592E+01 WEIGHT= 1.352790D+00 (SC-SC)
-EVDW2= 2.387106E+01 WEIGHT= 1.593040D+00 (SC-p)
-EES= -7.520330E+00 WEIGHT= 7.153400D-01 (p-p)
-EVDWPP= -2.624923E+01 WEIGHT= 1.137100D-01 (p-p VDW)
-ESTR= 8.665144E-27 WEIGHT= 1.000000D+00 (stretching)
-EBE= 1.082023E+00 WEIGHT= 1.138730D+00 (bending)
-ESC= 9.168846E+01 WEIGHT= 1.625800D-01 (SC local)
-ETORS= 2.664535E-15 WEIGHT= 1.985990D+00 (torsional)
-ETORSD= -2.547586E+00 WEIGHT= 1.570690D+00 (double torsional)
-EHPB= 0.000000E+00 WEIGHT= 1.000000D+00 (SS bridges & dist. cnstr.)
-ECORR4= -4.501075E+00 WEIGHT= 4.288700D-01 (multi-body)
-ECORR5= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
-ECORR6= 0.000000E+00 WEIGHT= 0.000000D+00 (multi-body)
-EELLO= 2.197932E+01 WEIGHT= 1.603600D-01 (electrostatic-local)
-ETURN3= -1.258124E+00 WEIGHT= 1.687220D+00 (turns, 3rd order)
-ETURN4= 9.498513E+00 WEIGHT= 6.623000D-01 (turns, 4th order)
-ETURN6= 0.000000E+00 WEIGHT= 0.000000D+00 (turns, 6th order)
-ESCCOR= 0.000000E+00 WEIGHT= 0.000000D+00 (backbone-rotamer corr)
-EDIHC= 0.000000E+00 (dihedral angle constraints)
-ESS= 0.000000E+00 (disulfide-bridge intrinsic energy)
-UCONST= 0.000000E+00 (Constraint energy)
-ETOT= 2.482802E+01 (total)
-
-Initial:
- Kinetic energy 3.16218E+01
- potential energy 2.48280E+01
- total energy 5.64498E+01
-
- maximum acceleration 7.07629E-01
-
- acceleration/energy drift too large 11.2926424070625
- 13.6605134887925 split increased to 2 itime 5488
- itsplit 1
- acceleration/energy drift too large 12.2479155916642
- 17.8916022742654 split increased to 2 itime 146134
- itsplit 1
- acceleration/energy drift too large 9.64402968286842
- 11.3087438689470 split increased to 2 itime 173097
- itsplit 1
- acceleration/energy drift too large 5.98151849708125
- 10.5358868963268 split increased to 2 itime 325094
- itsplit 1
- acceleration/energy drift too large 9.92185743247020
- 10.3282402848183 split increased to 2 itime 337991
- itsplit 1
- acceleration/energy drift too large 12.4467738353776
- 16.3475089599066 split increased to 2 itime 377718
- itsplit 1
- acceleration/energy drift too large 9.40536271695775
- 11.7402473647113 split increased to 2 itime 399086
- itsplit 1
- acceleration/energy drift too large 13.1653706876790
- 16.9150100267623 split increased to 2 itime 448471
- itsplit 1
- acceleration/energy drift too large 6.46490539699288
- 12.1544022140714 split increased to 2 itime 477390
- itsplit 1
- acceleration/energy drift too large 13.1589518405409
- 17.5436060457116 split increased to 2 itime 479111
- itsplit 1
- acceleration/energy drift too large 10.5950744430222
- 10.4028358818328 split increased to 2 itime 479526
- itsplit 1
- acceleration/energy drift too large 11.0521089342970
- 12.3123692023542 split increased to 2 itime 710277
- itsplit 1
- acceleration/energy drift too large 5.83156435721131
- 10.6993564628405 split increased to 2 itime 739656
- itsplit 1
- acceleration/energy drift too large 7.08760014331940
- 11.9290942024338 split increased to 2 itime 774367
- itsplit 1
- acceleration/energy drift too large 12.2797621496046
- 17.4776170393841 split increased to 2 itime 906363
- itsplit 1
- acceleration/energy drift too large 15.5956529698596
- 21.6103248292573 split increased to 2 itime 977004
- itsplit 1
-
-
-=================================== Timing ===================================
-
- MD calculations setup: 3.90625E-03
- Energy & gradient evaluation: 3.74867E+02
- Stochastic MD setup: 0.00000E+00
- Stochastic MD step setup: 0.00000E+00
- MD steps: 4.11719E+02
-
-
-============================ End of MD calculation ===========================
-CG processor 0 is finishing work.
- Total wall clock time 420.156250000000 sec
projects / unres.git / blobdiff